@Override
@Nonnull
public OffsetInfo next() {
try {
long indexOffset = countingInputStream.getByteCount();
int keysize = input.readUnsignedShort();
input.skipBytes(keysize);
Long dataOffset = input.readLong();
skipPromotedIndexes();
return new OffsetInfo(dataOffset, indexOffset);
} catch (IOException e) {
throw new IOError(e);
}
}
@Override
public int read(char[] cbuf, int off, int len) throws IOException {
int res = inReader.read(cbuf, off, len);
monitor.reportProgress(countingIn.getByteCount());
return res;
}
/**
* Start the parsing the file passed as parameter.
*
* @param file File to be parsed.
* @param progress Progress listener used to show the percent of completed task.
* @throws FileNotFoundException
* @throws IOException
* @throws InvalidFormatException
*/
public void parse(File file, ProgressListener progress)
throws FileNotFoundException, IOException, InvalidFormatException {
if (!file.exists())
throw new FileNotFoundException("File does not exists: " + file.getAbsolutePath());
HashSet<String> addedElements = new HashSet<>();
try (final CountingInputStream cntIs = new CountingInputStream(new FileInputStream(file));
final BufferedReader reader = new BufferedReader(new InputStreamReader(cntIs))) {
String line;
while ((line = reader.readLine()) != null && (line.startsWith("##") || line.isEmpty())) {}
if (line == null) throw new InvalidFormatException("File is empty");
Hashtable<String, Integer> header = parseHeader(line);
if (!header.containsKey(CHRPOS)
|| !header.containsKey(ALLELES)
|| !header.containsKey(ALLALLELECOUNT))
throw new InvalidFormatException("Header does not contain all necessary fields");
this.reader.setUp();
long length = file.length();
if (progress != null) progress.start(file.getAbsolutePath(), length);
long stime = (new Date()).getTime();
long seconds = 0;
int percent = -1;
while ((line = reader.readLine()) != null) {
if (line.isEmpty() || line.startsWith("#")) continue;
final String elements[] = line.split(DELIMITER);
if (elements.length != header.size())
throw new InvalidFormatException("Element does not have the same header size");
final String chromosomePosition = elements[header.get(CHRPOS)];
final String alleles = elements[header.get(ALLELES)];
final String allAlleleCount = elements[header.get(ALLALLELECOUNT)];
final String hash = chromosomePosition + alleles;
if (!addedElements.contains(hash)) {
readElement(chromosomePosition, alleles, allAlleleCount);
addedElements.add(hash);
}
float readLength = cntIs.getByteCount();
int newPercent = (int) ((readLength / length) * 100);
long diff = (new Date()).getTime() - stime;
long elapsedSeconds = diff / 1000;
if (percent != newPercent || seconds < elapsedSeconds) {
seconds = elapsedSeconds;
percent = newPercent;
if (progress != null)
progress.progress(file.getAbsolutePath(), percent, seconds, (long) readLength);
}
}
if (progress != null) progress.end(file.getAbsolutePath());
} finally {
this.reader.end();
}
}